Paul Bond

Computational Structural Biologist

University of York

Structural Biology Software Development X-ray Crystallography Data Analysis Machine Learning



Automated model-building pipeline for X-ray crystallography and cryo-EM


Interactively analyse thermal shift (DSF) data by fitting sigmoid curves


Virtual simulations of undergraduate analytical laboratory experiments


Compare anomalous scattering factors (f' and f") for different elements

Cluedo Solver

Input guesses and responses to work out the true suspect, weapon and location


A simple Pomodoro timer to help focus on tasks for 25 minute periods

Colour Evolution

Introduction to evolutionary algorithms using an evolving grid of random colours


Coot Workshop
A two-part workshop to introduce interactive model building in Coot

RNA Model Building Workshop
An introduction to the model building tools available in CCP4 for nucleic acid structures

CCP4 Molecular Graphics Tutorial
A tutorial covering most of the basic features of CCP4mg

Selected Publications

The CCP4 suite: integrative software for macromolecular crystallography
J Agirre, et al.
Acta Cryst. D, 79, 449 (2023)

ModelCraft: an advanced automated model-building pipeline using Buccaneer
P Bond, K Cowtan
Acta Cryst. D, 78, 1090 (2022)

Shift-field refinement of macromolecular atomic models
K Cowtan, S Metcalfe, P Bond
Acta Cryst. D, 76, 1192 (2020)

Predicting protein model correctness in Coot using machine learning
P Bond, K Wilson, K Cowtan
Acta Cryst. D, 76, 713 (2020)

See the full list on Google Scholar

Selected Presentations

Model Building and Density Modification
3rd Dec 2023: Diamond Light Source, UK
Overview of the Cowtan group programs for density modification and model building in CCP4: Parrot, Buccaneer, Nautilus and ModelCraft.

Automatic Model Building (CCP4 / CCP-EM)
9th Nov 2023: Spring-8, Japan
Overview of the automated model-building programs available in CCP4 and CCP-EM.